GreeNC

Gene information

This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.

Gene alias / name	Chrom.	Start	End	Assembly	Species	Details
Atauschii_AET4Gv20855900 [ AET4Gv20855900]	4D	518325106	518327774	v4	Aegilops tauschii (Ensembl Plants 51)	Coding? Yes

Transcript features

This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.

Transcript alias / name	Confidence	Pre-miRNA	Length	Orthologous group	Sequence	Details
Atauschii_AET4Gv20855900.1 AET4Gv20855900.1	Low	No	575	OG0010024		Get ORF Coding potential... Type: noncoding Potential: -0.828 Folding energies... MFEI: -32.191 AMFE: -0.615 GC content %: 52.348
Atauschii_AET4Gv20855900.2 AET4Gv20855900.2	Low	No	699	OG0010024		Get ORF Coding potential... Type: noncoding Potential: -0.700 Folding energies... MFEI: -34.063 AMFE: -0.632 GC content %: 53.934
Atauschii_AET4Gv20855900.3 AET4Gv20855900.3	High	No	486	OG0010024		Get ORF Coding potential... Type: noncoding Potential: -0.755 Folding energies... MFEI: -37.305 AMFE: -0.641 GC content %: 58.230
Atauschii_AET4Gv20855900.4 AET4Gv20855900.4	Low	No	522	OG0010024		Get ORF Coding potential... Type: noncoding Potential: -0.741 Folding energies... MFEI: -37.797 AMFE: -0.634 GC content %: 59.579
Atauschii_AET4Gv20855900.6 AET4Gv20855900.6	High	No	338	OG0075707		Get ORF Coding potential... Type: noncoding Potential: -1.069 Folding energies... MFEI: -36.065 AMFE: -0.616 GC content %: 58.580

Matches to external databases

The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.

Transcript alias	Database	Version	Hit	Evalue
Atauschii_AET4Gv20855900.2	SwissProt	2021-04-01	Q5ZLV2	4.51e-6
Atauschii_AET4Gv20855900.4	SwissProt	2021-04-01	Q5ZLV2	2.16e-6
Atauschii_AET4Gv20855900.1	RepBase (RepeatMasker)	2014-01-31	LINE/Jockey
Atauschii_AET4Gv20855900.2	RepBase (RepeatMasker)	2014-01-31	LINE/Jockey

Gene models

Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).